What is the source format of the stuff? Also, when you say you can hear the audio, is it clear or are there any disturbances? To what specific CoDec do you render? If you render uncompressed, it's well possible that the data rates are simply too high and the system can't keep up. It also is important, where you play the file. Have you tried alternate player software like WinAmp, VLC or VirtualDub even?

Avastjonny: It's very important that you provide more information, as the other forum members are requesting in order to help.

What AE version are you using? What format is your audio? Is it a separate audio file or is it embeded in a video file?

FWIW, in After Effects CS3 and later, MP3 audio is supported (it's actually converted to PCM, ie WAV/AIFF in import). In previous versions, yes, converting to AIFF/WAV would be a good idea? Other compressed formats, like AAC, could be a problem.

what if you export your audio alone in wav or aiff, and then reimport it into after effect, add it to your time line, disable the audio from your video file and export. DO you still have your audio cut out ?